Not a simple issue, I feel for you... So a couple of questions and I'll give give you my best guess on how to deal with it. Maybe someone will have a better idea. And sorry, I'm thinking of all the variables, so this won't be a short reply. Let me run off some questions comments and then some thoughts. Get back to us with any answers to my questions, which may give someone a better idea than my first attempt.
NOTE: BACKUP FIRST!!! Maybe even pull an extra copy of the Company File to your Desktop!!!
NOTE: Don't Delete anything until you get down to my Delete comments below!!!
Since your Reconciling, I'm assuming this is a Checking Acct. Let me know if it's Credit Card, Savings or some other account. But for this Acct, does your monthly Reconciliation end up with a $0 balance and everything matches (that should match)?
When you get done Reconciling, is the actual Acct Balance in QBs way off from what the Bank shows? If it matches, is it possible the Unreconciled transactions may just be duplicate entries.
If you look at the Unreconciled transactions and then look around at the other transactions before and after, do you see any matches. For Deposits, it's possible someone grouped a few checks together, so you may have one Unreconciled item that matches a few other individual deposits or the other way around.
You might look at the Undeposited Funds Account for the same time and see if anything stands out. You might also look at the Deposits around that time an see if the associated Account stands out. There could be a Deposit directly to Sales and not associated with a Invoice Payment, etc.
Similar idea with the Payments out. Is there anything off about the Check Numbers or Vendor Name? Is there anything in the Memo field that you make you think the entry came from a Bank Feed or was manual entered. Anything off with the associated Account here too. Are any of them just Accounts Payable and not associated with paying a Vendor Invoice?
If you do find duplicates or individual entries that match other single ones, take your time to figure out which one is correct. It may or may NOT be the Reconciled item. Right Click on the Check and choose Edit. See if you can confirm which one is attached to an Invoice, etc. and is the correct entry. Once you've done that, Delete the incorrect entry.
When you are done Deleting, then take the LAST Statement that you reconciled. Put in the date and amount of that statement. Check off ONLY the items that you have just corrected and the Balance should come back to $0. You can do this process a few times if you want to, just be sure not to check off and Reconcile any extra transactions.
If you get all done and you still have extra items. Then I'd make and Journal Entry to bring the QBs Account in Balance with the Bank Account and then do the above Reconciliation again with the last statement and clear out these entries.
You may want to check with your CPA on where they want the Journal Entry and what date. I'd guess 01/01/22, but you should check with them.
Hope this helps. Get back to us with any results or other questions & info.